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<!DOCTYPE html>
<html lang="en">
<head>
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<title>ReproNim</title>
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<body>
<div id="wrapper">
<section class="section-1">
<header class="site-header">
<div class="container">
<div class="row">
<div class="col-sm-4 col-xs-8">
<h1 class="logo"><a href="index.html">ReproNim</a></h1>
</div>
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<nav class="navbar pull-right" role="navigation">
<!-- Brand and toggle get grouped for better mobile display -->
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<div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
<ul class="nav navbar-nav">
<li><a href="discover.html">Discover</a></li>
<li><a href="describe.html">Describe</a></li>
<li><a href="do.html">Do</a></li>
<li><a href="teach.html">Teach</a></li>
<li><a href="community.html">Community</a></li>
</ul>
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</div> <!-- container -->
</header> <!-- site header -->
<div class="container">
<img src="images/logo-square-256.png" alt="ReproNim logo" />
<h1 class="promo-text">ReproNim: A Center for Reproducible Neuroimaging Computation</h1>
</div>
</section>
<section class="section-2">
<div class="container">
<h2 class="section-heading text-center">Welcome to ReproNim!</h2>
<div class="row">
<div class="col-md-4">
<p>
The ReproNim vision is to to help neuroimaging researchers to:
</p>
<ul>
<li>Find and Share data in a <a class="text-danger" href="http://www.nature.com/articles/sdata201618">FAIR</a> fashion (<strong>discover</strong> resources with <strong>NeuroBLAST</strong>)</li>
<li>Comprehensively describe their data and analysis workflows in precisely replicable fashion (<strong>describe</strong> research processes with ReproIN and <strong>BrainVerse</strong>)</li>
<li>Manage their computational resource options (<strong>do</strong> analysis with <strong>NICEMAN</strong>)</li>
</ul>
<p>
so that the outcomes of neuroimaging research are more reproducible.
</p>
</div>
<div class="col-md-8">
<img class="overview" src="flow.svg" alt="Data flow diagram" />
</div>
</div>
</div>
</div>
<div class="container">
<div class="row">
<div class="col-md-12">
<p>
Achieving these goals requires both technical development of readily accessible, user-friendly computational services (discover, describe, and do functions) that can be readily integrated into current research practices, and broad educational outreach about reproducibility (teach) to the neuroimaging community at large including developers as well as applied researchers across basic sciences and clinical disciplines.
</p>
<h3>Breaking News</h3>
<p>
<ul>
<li> <a href="https://www.repronim.org/"><strong> ReproNim</a> and <a href="http://schizconnect.org/">SchizConnect</a> - A Project-Centered Example of Containers and Semantic Markup </strong> <a href="https://docs.google.com/document/d/14j0D28ZcyNZGedGIS9AlvRpHciPXkzE6uiqYQgqdLtI/edit?usp=sharing">(Agenda)</a>
<ul>
<li> <strong>Session 1, Friday October 4, 2019, 2-3:30pm EDT </strong> 1.5 Hour Webinar with SchizConnect and ReproNim faculty
<ul>
<li> Introduction to the <a href="http://schizconnect.org/"> SchizConnect</a> Project, Semantic Markup, and Containerized Workflows
<li> <em>[video conference open to the public]</em>
<li> Connect by Zoom: <a href="https://umassmed.zoom.us/j/822880060">https://umassmed.zoom.us/j/822880060</a> , or see <a href="https://docs.google.com/document/d/14j0D28ZcyNZGedGIS9AlvRpHciPXkzE6uiqYQgqdLtI/edit?usp=sharing"> Agenda</a> for additional details
</ul>
<li> <strong> Session 2, Friday October 18, 2019, 9am-5pm CDT</strong>, Full day Workathon with SchizConnect and ReproNim faculty
<ul>
<li> Containerized Workflows and Semantics: Project Integration/Tools Applications
<li> <em>[video conference open to the public]</em>
<li> Connection details will be announced when available
</ul>
</ul>
<li> A few highlights from <a href="https://escience2019.sdsc.edu/">IEEE eScience 2019</a> in San Diego, CA
<ul>
<li> Keynote lecture by project leader Maryann Martone:<a href="https://escience2019.sdsc.edu/keynote/martone/"> Neuroscience as an open, FAIR and citable discipline</a>
<li> The <a href="https://researchobject.github.io/ro2019/">RO2019 Workshop in Research Objects</a>
<ul>
<li> ReproNim presents <a href="https://zenodo.org/record/3336609#.XYFRaSUpC-w">The ReproPub</a> A hybrid research object for supporting publication-level re-execution and generalization of neuroimaging research findings
<li> External Advisory Board member Daniel Katz presents <a href="https://zenodo.org/record/3338176#.XYFRFCUpC-w">Citation and Research Objects: Toward Active Research Objects</a>
</ul>
</ul>
<li> ReproNim joins in a <a href="https://www.isi.edu/events/calendar/12756">Reproducibility Colloquium at USC</a>, September 23, 2019
<li> Maryann Martone shares her expertise on "Harnessing the Power of Cloud Technology to Propel Neuroscience Research Forward" at the National Academies of Science <a href="http://www.nationalacademies.org/hmd/Activities/Research/NeuroForum/2019-SEP-24.aspx">Neuroscience Data in the Cloud Workshop</a> September 24, 2019 in Washington, DC.
<li> Great meeting at <a href="https://www.neuroinformatics2019.org/">INCF NeuroInformatics 2019</a>
<ul>
<li> External Advisory Board member <a href="https://www.research.manchester.ac.uk/portal/en/researchers/carole-goble(bcd47b34-dc6d-42d5-8561-7a4cd64f07c0).html"> Carole Goble</a> gives Plenary Lecture!
<li> <a href="https://docs.google.com/document/d/1Lu-q_fBsfnivfzVQgTBbpaF0Ori9deI0XxsgCMs90bo/edit?usp=sharing">ReproNim Presentations</a>
<li> NIDM/BIDS Scientific Interest Group (SIG) Meeting
</ul>
<li> <a href="https://f1000research.com/documents/8-1329/">BIDS and the NeuroImaging Data Model</a>: joint statement of complementary standards and synergistic technologies, <em>F1000 Research, August 1, 2019</em>
<li> New Publication: <a href="https://www.frontiersin.org/articles/10.3389/fninf.2019.00001/full">The ReproNim Perspective on Reproducible Neuroimaging</a>
</ul>
</p>
<p><a href="news_archive.html"><strong>News History</strong></a>
</p>
<h3>Use cases</h3>
<p>
ReproNim tools and services are intended to support a wide range of users with varied background, from <em>applied users</em> with minimal or extensive experience in image analysis, physics, and computer science to <em>technology developers and software engineers</em>.
</p>
<p><a href="use_cases.html">Read more</a>.</p>
</div>
</div>
</div>
</section>
<section class="section-3">
<div class="container">
<div class="row">
<div class="col-sm-4">
<h3><a href="discover.html">Discover</a></h3>
<p>
On-demand access (discovery) for widely distributed web-based data, publication and software resources, with highly refined search tools. There are two broad classes of product we envision:
</p>
<ul>
<li>Tools to help researchers Publish their data, making it discoverable</li>
<li>Tools to help researchers Discover published data.</li>
</ul>
<p>
These tools are designed to facilitate data sharing, use and discovery. ReproNim is developing an integrated application, <strong>NeuroBLAST</strong>, that will powerfully enable user-specified search and publish functions to data repositories, published studies, versioned software packages, study-related questions, and content.
</p>
<p><a href="discover.html">Read more.</a></p>
</div>
<div class="col-sm-4">
<h3><a href="describe.html">Describe</a></h3>
<p>
Reproducible description based on recording, reporting, and reusing experimenter procedures from start to finish. Machine-captured experimental metadata from scanner (data acquisition) to methods, analyses, and results.
</p>
<ul>
<li>Tools to help researchers record (describe) experimental procedures</li>
<li>Tools to help researchers define and semantically describe workflow.</li>
</ul>
<p>
ReproNim is developing <strong>BrainVerse</strong> to help researchers manage, track and share information in a comprehensive format.
</p>
<p><a href="describe.html">Read more.</a></p>
</div>
<div class="col-sm-4">
<h3><a href="do.html">Do</a></h3>
<p>Efficient management of data and scripts while capturing the
history and details of changes and analyses execution in a fashion
that facilitates inspection, comparison, modification, sharing, and
re-execution. We provide</p>
<ul>
<li>Support, maintenance, and promotion of platforms
(e.g., <a href="http://neuro.debian.net">NeuroDebian</a>) and
tools (e.g., <a href="http://singularity.lbl.gov">Singularity</a>
and <a href="http://datalad.org">DataLad</a>) for efficient and
reproducible computation and data management
</li>
<li>Tools and materials to establish reproducible computation across
all stages of the neuroimaging research</li>
</ul>
<p>
ReproNim is developing <strong>ReproIn</strong> framework for turnkey
collection of BIDS datasets straight from the
scanner, and <strong>NICEMAN</strong> to help researchers
track and manage computation resources that they have available and to
use them in a reproducible and scalable way.
</p>
<p><a href="do.html">Read more.</a></p>
</div>
</div> <!-- row -->
</div>
</section> <!-- section-2 -->
<section class="section-4">
<div class="container">
<div class="row">
<div class="col-md-12">
<h2 class="section-heading text-center"><a class="fragment-identifier" name="training">Teach</a></h2>
<p>An increasing body of evidence point to some issues in reproducibility in biomedical or life sciences. The issue of lack of reproducibility has been now described in several scientific domains and for several years, raising concerns in the scientific community. ReproNim has developed a curriculum that will give researchers the information, tools and practices to perform repeatable and efficient research and a map of where to find the resources for deeper practical training. </p>
<p><a href="teach.html">Read more.</a></p>
</div>
</div>
</div>
</section>
<section class="section-5">
<div class="container">
<div class="row">
<div class="col-md-12">
<h2 class="section-heading text-center"><a class="fragment-identifier" name="training">Tools</a></h2>
<p>We have many tools designed to help the user work through a more reproducible version of their data analysis tasks. These toold support areas such as Data processing, Data ingestion, Standardization, Search, Data Management, Computation, Testing, etc. </p>
<!-- <p><a href="reprostack.html">Read more.</a></p> -->
<p><a href="https://docs.google.com/document/d/1I1qFuo6aemiZRUGS4KLJF2qieNXGQS1Gr-u_ti8ZK78/">Read more.</a></p>
</div>
</div>
</div>
</section>
<section class="section-6">
<div class="container">
<div class="row">
<div class="col-md-12">
<h2 class="section-heading text-center">Community</h2>
<p>
ReproNim is only as successful as the neuroimaging community itself. We encourage active participation and engagement in our efforts. See our current <a href="community.html">community collaborator and service projects</a>.
</p>
<p>
Join us! If you have a project that could benefit from a collaborative relationship with ReproNim let us know your interests and needs via email at <a href="mailto:[email protected]">[email protected]</a>. Someone from ReproNim will be in touch to see how we can work together.
</p>
</div>
</div>
<div class="row">
<div class="col-md-12">
<h3 class="section-heading text-center">Community events</h3>
<div id="events">Loading events...</div>
<div id="more_events"><a href="events.html">See more...</a>.</div>
</div>
</div>
</div>
</section>
<div class="section-7">
<div class="container">
<div class="row">
<div class="col-md-12">
<h2><a class="fragment-identifier" name="contact-us">Contact</a></h2>
<p><b>Email us</b> at <a href="mailto:[email protected]">[email protected]</a></p>
<p><b>Read our blog</b> at <a href="https://repronim.wordpress.com/">https://repronim.wordpress.com/</a></p>
<p><b>Find us on Twitter</b> at <a href="https://twitter.com/repronim">@ReproNim</a></p>
<p><b>Get updates</b> by <a href="https://docs.google.com/forms/d/e/1FAIpQLScLkBb-V2XK3eOH6gE95lburchjait4-vs57z1ry_5oYp8O0w/viewform">signing up for our mailing lists</a></p>
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